+Open data
-Basic information
Entry | Database: PDB / ID: 109m | ||||||
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Title | SPERM WHALE MYOGLOBIN D122N ETHYL ISOCYANIDE AT PH 9.0 | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / LIGAND BINDING / OXYGEN STORAGE / OXYGEN BINDING / HEME | ||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Smith, R.D. / Olson, J.S. / Phillips Jr., G.N. | ||||||
Citation | Journal: Thesis, Rice / Year: 1999 Title: Correlations between Bound N-Alkyl Isocyanide Orientations and Pathways for Ligand Binding in Recombinant Myoglobins Authors: Smith, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 109m.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb109m.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 109m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/09/109m ftp://data.pdbj.org/pub/pdb/validation_reports/09/109m | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17365.164 Da / Num. of mol.: 1 / Mutation: INS(M0), D122N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Tissue: SKELETAL MUSCLE / Cellular location: CYTOPLASM / Organ: SKELETALSkeleton / Plasmid: PEMBL 19+ / Production host: Escherichia coli (E. coli) / Strain (production host): PHAGE RESISTANT TB1 / References: UniProt: P02185 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-ENC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.9 % |
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Crystal grow | pH: 9 Details: 3.0 M AMMONIUM SULFATE, 20 MM TRIS, 1MM EDTA, PH 9.0 |
-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1993 / Details: PINHOLE COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→6 Å / Num. obs: 15743 / % possible obs: 80.7 % / Observed criterion σ(I): 0 / Redundancy: 4.35 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.044 |
Reflection shell | Resolution: 1.83→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.268 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SPERM WHALE MYOGLOBIN 0M, D122N (DEOXY) Resolution: 1.83→5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 20.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
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Xplor file |
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